Run ID: SRR22048484
Sample name:
Date: 2024-04-14T15:23:14.352225
Number of reads: 2069142
Percentage reads mapped: 94.02
Median coverage: 67.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | RD219 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491695 | c.913C>T | synonymous_variant | 1.0 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
Rv0565c | 657237 | p.Glu78Asp | missense_variant | 1.0 | ethionamide | |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.13 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.13 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.11 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473252 | n.1407T>C | non_coding_transcript_exon_variant | 0.13 | streptomycin | Uncertain significance |
kanamycin | Not assoc w R | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1473259 | n.1414C>T | non_coding_transcript_exon_variant | 0.12 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.99 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
rrl | 1475883 | n.2226A>C | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475884 | n.2227A>G | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475896 | n.2239A>G | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
linezolid | ||||||
rrl | 1475897 | n.2240T>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475898 | n.2241A>G | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475899 | n.2242G>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475906 | n.2249C>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475916 | n.2259C>G | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475937 | n.2280A>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475943 | n.2286G>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475945 | n.2288C>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
linezolid | ||||||
rrl | 1475952 | n.2295A>G | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.11 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
PPE35 | 2168428 | c.2184delG | frameshift_variant | 1.0 | pyrazinamide | Uncertain significance |
PPE35 | 2168905 | p.Ile570Val | missense_variant | 1.0 | pyrazinamide | |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv1979c | 2223491 | c.-327C>A | upstream_gene_variant | 0.99 | clofazimine | Not assoc w R |
bedaquiline | Uncertain significance | |||||
folC | 2746275 | p.Val442Phe | missense_variant | 1.0 | para-aminosalicylic_acid | |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 0.99 | ethionamide | Uncertain significance |
embC | 4238972 | c.-891C>G | upstream_gene_variant | 1.0 | ethambutol | Uncertain significance |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
gid | 4407678 | c.525G>C | synonymous_variant | 1.0 | streptomycin | Not assoc w R - Interim |